3F29

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.174 (Depositor) 
  • R-Value Work: 
    0.154 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase

Trofimov, A.A.Polyakov, K.M.Tikhonova, T.V.Popov, V.O.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eight-heme nitrite reductase
A, B
525Thioalkalivibrio nitratireducensMutation(s): 0 
EC: 1.7.2.2
UniProt
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2))
Explore L0DSL2 
Go to UniProtKB:  L0DSL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0DSL2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
C [auth A]
D [auth A]
E [auth A]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PG6
Query on PG6

Download Ideal Coordinates CCD File 
GA [auth B],
HA [auth B],
N [auth A]
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
IA [auth B]
JA [auth B]
KA [auth B]
LA [auth B]
MA [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO3
Query on SO3

Download Ideal Coordinates CCD File 
CA [auth B],
FA [auth B],
K [auth A]
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
DA [auth B],
EA [auth B],
L [auth A],
M [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.174 (Depositor) 
  • R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.568α = 90
b = 193.568β = 90
c = 193.568γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-10-22
    Changes: Derived calculations
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-11-06
    Changes: Structure summary